For new amino acids you can use:
set_add_terminal_residue_default_residue_type("UNK")
Then you get an UNK (no CB) instead of ALA.
As for mutation, you have to go via ALA and then rename it.
Alternatively you can append UNK to your standard-residues.pdb (found in
$COOT_PREFIX/share/coot/). Then you can use UNK in "mutate" functions. I
(*) am reluctant to add it to the amino acids for all since the PDB
(nowadays) says
(http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_chem_comp.three_letter_code.html):
For ambiguous polymer components three-letter code should be given as 'UNK'.
So UNK is not only for (unknown) amino acids any more...
B
(*) Not sure what Paul thinks
On 27/06/2015 19:02, Ethan Merritt wrote:
On Saturday, 27 June 2015 04:39:56 PM Clarke, Oliver wrote:
I would still ultimately favor making it a standard residue with three letter
code UNK and single letter code X - it allows for easy specification of
ambiguity, and it is the PDB-sanctioned way of representing an amino acid of
unknown identity.
I would also suggest being able to set this as the default type for new
residues - it allows easy recognition of amino acids that are as yet
unassigned, and avoids confusion with alanine.
I like that idea a lot.
Ethan
Cheers,
Oliver.
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Dr. Bernhard Lohkamp
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Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
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